Systematic review of mRNA expression in human oocytes: understanding the molecular mechanisms underlying oocyte competence

The biggest cell in the human body, the oocyte, encloses almost the complete machinery to start life. Despite all the research performed to date, defining oocyte quality is still a major goal of reproductive science. It is the consensus that mature oocytes are transcriptionally silent although, during their growth, the cell goes through stages of active transcription and translation, which will endow the oocyte with the competence to undergo nuclear maturation, and the oocyte and embryo to initiate timely translation before the embryonic genome is fully activated (cytoplasmic maturation). A systematic search was conducted across three electronic databases and the literature was critically appraised using the KMET score system. The aim was to identify quantitative differences in transcriptome of human oocytes that may link to patient demographics that could affect oocyte competence. Data was analysed following the principles of thematic analysis. Differences in the transcriptome were identified with respect to age or pathological conditions and affected chromosome mis segregation, perturbations of the nuclear envelope, premature maturation, and alterations in metabolic pathways—amongst others—in human oocytes.


Introduction
Chromosome aberrations which occur along nuclear maturation during oogenesis are the major, but not single, determinants of poor oocyte quality.During its genesis and differentiation process, the female oocyte coordinates appropriate chromosome segregation and ooplasm and molecular organisation (cytoplasmic maturation).Although the latter process is poorly understood, it is known to involve a physical growth of the oocyte, provided by the active synthesis of macromolecules, proteins and stage-specific and timely messenger RNAs (mRNA) and their specific posttranslational modification [1].mRNAs work as templates of genes which move from the nucleus of the cell to the cytoplasm, where they will be translated to a series of amino acids to subsequently form proteins.Therefore, protein expression is linked to mRNA quantity, which is conditioned by the equilibrium of transcription rates (the process of making RNA copies from DNA gene sequences) and decay.However, studies have shown that it is not only quantity but posttranscriptional modifications of mRNAs such as capping, splicing and polyadenylation that govern mRNA storage, recruitment, translation and decay during oocyte maturation and early embryogenesis [2][3][4].A global shift in maternal mRNA translation, which is crucial for meiotic progression, fertilization, and embryo development, has been reported to coincide with the oocyte's re-entry into the meiotic cell cycle [5].This switch involves the repression of mRNAs that are highly active in quiescent oocytes and the activation of mRNAs that were repressed.In the recent years, the use of single-cell RNA sequencing (scRNA-seq) technology has contributed to investigating transcriptional differences in oocytes [6].Through the present systematic review, authors aim to identify quantitative differences in transcriptome of human oocytes that may link to patient demographics that could affect oocyte competence.

Design and search strategy
A systematic review was performed to allow the identification, screening, and summary of published research findings in a structured and reproducible method.Such analysis was conducted across three electronic databases (MEDLINE, EMBASE and Google Scholar).A manual search of original articles was also performed to allow integration of further studies.The latest search was carried out on 20/03/2023.The search terms used were as follows: messenger RNA OR mRNA AND profiling OR gene expression OR transcripts AND quantitative OR research article AND oocyte OR egg AND quality OR competence OR development OR maturation OR fertilisation OR embryo OR outcome AND human.
The study selection process followed the PRISMA (preferred Reporting Items for Systematic Reviews and Meta-Analysis) guidance [7].Search results from the three databases were compared and duplicates were removed.Furthermore, results were screened by title and abstract to establish relevance for the present review.The search was also performed by a second person to corroborate the results.
Inclusion criteria for studies were as follows: • Original research articles, publication in peer-reviewed journals.• Recent publication date (2015-2023).
• Include the study of human oocytes and their mRNA content.
Exclusion criteria for studies were as follows: • Article not accessible in English.

Quality assessment
KMET score was used to critically appraise eligible articles as described by Kmet et al., 2004 [8].This allows the assessment of quantitative research based on 14 criteria, each of them is scored as "not met/not applicable" (0 points), "partially met" (1 point) or "met" (2 points).The total score is converted to a percentage (over a maximum of 28 points).As described by Kmet et al. (2004) a low cut-off point of 55% was used as an inclusion/exclusion parameter.

Data extraction and synthesis
Table 1 summarises the study details, including purpose, methodology, genes studied, cohort description, main findings and quality assessment score.Quantitative data derived from the included studies was analysed following a thematic analysis approach [24], allowing the identification across different study designs to be combined and understood.

Results
The initial search from the three databases resulted in 505 records, once duplicates were removed.After screening by title and abstract, a total of thirty-two publications were subjected to the eligibility criteria and seventeen were further appraised using KMET quality score.Fifteen original articles were included for data extraction and analysis (Fig. 1).

Study characteristics
Table 1 contains the synthesis for the included studies.A total of six studies were performed in China while other studies were included for each of the following countries: United States (n=2), Spain (n=3), Italy (n=2), and Iran (n=2).The majority (14/15, 93.3%) based their results on single cell approaches for human oocytes and only one study used pooled oocytes.Moreover, ten studies performed a comprehensive sequencing whereas a minority (5/15, 33.5%) looked into specific genes.The KMET score of the included quantitative studies ranged from 60 to 92%.The main limitation found were limited sample size, control for confounding variables and lack of report of estimate of variance for the main results.Oocyte maturation (including regulation of cell cycle progression and cellular metabolism) is the most studied theme, being included in twelve out of the fifteen selected studies.Genes involved in fertilisation, and embryo development were discussed in four and three research studies, respectively.

Regulation of the cell cycle progression
Oocyte maturation is the culmination of an intermittent process which involves two arrests during the meiotic cycle (prophase I and metaphase II) together with changes at a cytoplasmic level.Resumption of the cell cycle is orchestrated by cytoplasmic factors, but its progress depends on checks for adequate environmental conditions, DNA integrity, DNA replication completeness and chromosome spindle attachment [25].High concentrations of cyclic adenosine monophosphate (cAMP) are imperative to keep the cycle arrested.Cyclin-dependant kinases (Cdk), together with cyclins, drive the cell cycle forward once cAMP levels decline [26].The maturation-promoting factor (MPF) is a Cdk-cyclin complex that targets the nucleoplasm and is activated in nucleoplasm (such as by SGK1 [27]) thus promoting chromosome condensation and nuclear envelope breakdown as an initial step in prophase I that precedes spindle formation and progression to metaphase I.A comparison of expression profiles in 120 GV stage oocytes with and without cytoplasmic transfer (CT) from MII-stage oocytes at retrieval day, was performed to evaluate the cytoplasmic effect to promote maturation in immature eggs [10].The authors showed that meiosis resumption involves not only specific gene expression but also has a time-dependant dimension as culture for 24h of GV oocytes improved CDC25 and AURKC expression and meiosis progression compared Day 0 GVs (regardless of CT).Interestingly, expression of DNA repair transcripts (BRCA1, ATR and ATM) showed to be increased after 24h culture, suggesting that DNA repair was active at that stage, which was not observed in immature oocytes at the day of retrieval.DNA repair, rather than apoptosis, was suggested as inhibitors of apoptosis such as neural apoptosis protein (NAIP) exhibited increased expression [10].Related to nuclear maturation, research has shown that AURK transcripts are overexpressed in women with increased body mass index, which could explain described spindle abnormalities in oocytes (as shown by Machtinger et al., 2012) [23,28].
Additionally, overexpression of DPYD (a NADP+ -dependent enzyme encoded with a role in the repair of DNA double strand breaks) has been reported in in vitro (IVM) studies, showing that oocytes have compensatory mechanisms to minimise maturation failure [18].A study of nine human MII showed that, the biological processes that showed the most differential enrichment between old and young oocytes were those related to ubiquitination and the ubiquitination-related pathway, including the mitotic cell cycle and meiosis [22].The overexpression in older patients of key transcripts such as CDC34, UBA1, and UBE2C, as well as the under expression of the hub gene SKP1, are associated with an enrichment in the "Ubiquitin-mediated proteolysis" pathway.The authors explain that elevated levels of UBE2C result in the premature activation of the APC and cytokinesis, hence disrupting the meiotic cycle.
MAPK activity could be inhibited in presence of oxidative stress, and DUSP1 overexpression could play a part in this cause-effect phenomenon as described in woman with endometriosis [17].In the same study, looking at 32 MIIstage oocytes from healthy versus woman with endometriosis, it was found that WEE1 was upregulated in the latter group.Together with DUSP1 and WEE1, other genes such Fig. 1 PRISMA Flowchart.Summarised detailed the database searches, the number of studies screened, and the full texts retrieved as ID4, G0S2, and CYP26A1 could be useful as markers to understand meiotic maturation inhibition rates in oocytes [17,19].Using a single-cell transcriptomic approach, obesity resulted in differential gene expression along different maturation stages [15].DUSP1 was also shown to be upregulated together with the inflammatory gene CXCL2 whereas TWIST1, ID3, GAS, and TXNIP were downregulated.Ovarian proinflammatory signalling is poorly understood in the context of oocyte maturation.
Relevant to meiosis II arrest maintenance via protein kinase C (PKC) inhibition, ANXA5 over expression in 36 vitrified/warmed mature oocytes has been hypothesised to contribute in younger females with good ovarian follicle count (AFC), which could be a favourable marker linked with prevention of premature granule exocytosis [13].Low AFC, associated with increased risk of infertility, showed an increased expression of a microtubule-severing enzyme (Fidgetin, FIGN), which could represent a marker of developmental quality in oocytes and could be related to oocyte aneuploidy.Analysis of genes associated to age and genome integrity on 20 MII-stage oocytes showed a non-significant decreasing trend of expression of genes belonging to the cohesin pathway (ESCO1, ESCO2, ESPL1, MAU2, SMC1A, SMC1B, and STAG3) in the ≥35 years age group [20].In the same research, it was found that REEP4 (encoding for a microtubule-binding protein) is down-regulated in elder patients, which could induce chromosome mis segregation and perturbations of nuclear envelope.
An interesting gene whose expression may respond to metabolic changes and induce spindle abnormalities is ECAT1, coding for a subunit of the subcortical maternal complex [29].It has been predicted to be a maternal gene as its mRNA is highly expressed at the GV stage and decreases throughout oocyte maturation, being almost absent in preimplantation embryos [11].Its function as a regulator of the cell cycle has been hypothesised since its downregulation using short interfering RNAs resulted in less oocytes undergoing germinal vesicle break down (GVBD).Moreover, it is thought that ECAT1 could impair SAC function as knockdown model results in higher rates (88%) of abnormal spindles in MII-stage oocytes compared to the control group (33%).Securin and beta-tubulin subunit proteins encoding genes (PTTG1 and TUBB8) were highly expressed in mature oocytes when compared to immature stages, which are relevant to chromosome segregation and maturation progression [21].
Cytoplasmic polyadenylation plays a critical role in controlling the stability and translation of maternal-effect mRNAs during oogenesis.Research has shown that a decrease in CPEB2 mRNA levels with aging may be associated with the diminished quality of mature MII oocytes that were subjected to in vitro maturation, leading to impaired protein production [23].The authors also identified the zinc finger transcription factor BNC1 as a potential upstream regulator in in vitro matured (IVM) MII-stage oocytes, which could establish a relationship between deficient nuclear maturation and ageing.In the same study, SON was identified as another potential master regulator.SON is responsible for encoding an RNA-binding protein that promotes pre-mRNA splicing, especially in transcripts with weak splice sites and those involved in cell cycle and DNA-related processes [23].

Cellular metabolism
Like any other cell type, oocytes require complex sequences of controlled biochemical reactions in order to sustain life and viability.An increasing research in metabolomics has been noted in the IVF field in order to identify and quantify intracellular and extracellular metabolites to, in turn, define the environment and understand its relationship with oocyte competence.Mitochondria are the major site for energy generation (ATP) in cells since a large number of enzymes involved in different metabolic pathways are contained within their matrix (Fig. 2).The cumulus cells in presence of functional gap-junction communication support the oocyte with sufficient amounts of pyruvate, lactate, and nicotinamide adenine dinucleotide phosphate (NADPH) [30].
Related to the function and mitochondrial performance in human oocytes, comparison of 10 GV, 9 MI and 8 MII-stage oocytes revealed increasing levels of TFAM, NRF1, and MT-CO1 gene expression along maturation stages [9].NRF1 and TFAM genes regulate mitochondrial DNA (mtDNA) copy number, thus providing an adequate energetic pool in oocytes required for homeostasis maintenance and regulation of survival.Also related to mitochondrial function, ATPase6 gene has been suggested as a marker of maturation since its transcript level is higher in IVM compared to immature oocytes [10].It is noteworthy to highlight that some metabolic pathways and related genes have been shown to be significantly impaired in IVM oocytes [18].Using qPCR, authors found that in IVM oocytes compared with the control group, expression of ACAT1 and HADHA was considerably reduced, whereas DPYD expression was high.ACAT1 and HADHA genes shared eight metabolic pathways and their deficient expression resulted in acetyl-CoA and succinate production blockage, resulting in declining the energy metabolism.The same study showed that ATP content of IVM oocytes was significantly reduced with the aid of immunofluorescence.This aberrant metabolic environment was also suggested to not only impair ATP production but also calcium signalling.Interestingly, authors showed a compensatory mechanism based on nicotinamide nucleotide transhydrogenase (NNT) transcript level, where NADP+ and NADH are generated -although this does not correspond to the predicted transcriptional silencing during maturation.
Mitochondria-related genes such as COX6B1, COX8A, COX4l1, and NDUFB9 have been shown to be highly expressed in healthy MII-stage oocytes compared to immature oocytes [19].Remarkably, authors showed that in patients with polycystic ovary syndrome, immature oocytes highly expressed those genes suggesting a premature activation of oxidative phosphorylation process in mitochondrial function.The aberrant status of mitochondrial energy metabolism in this scenario highlighted the connection between metabolism and oocyte quality.Other research has shown downregulated expression of genes involved in oxidative phosphorylation pathways in the context of oocyte ageing [22].Cell-surface receptors such as G-protein-coupled receptors (GPCRs) play a pivotal role in metabolic processes as they catalyse the synthesis of cAMP from molecules of ATP.These GPCRs have been shown to be age-sensitive in human oocytes [20].Dysregulated expression could lead into premature meiotic resumption, thus compromising oocyte quality as showed in other animal models [31].
Commonly stored in the form of droplets, lipids provide a vast potential energy reserve in oocytes.The increased gene expression of apolipoprotein E (APOE), involved in the metabolism of lipids, has been noted in patients with endometriosis compared to healthy woman.Given its role in lipoprotein metabolism and lipid transport, APOE overexpression could translate in increased lipid metabolism resulting in increased oxidative stress [17].In the same cohort, authors described upregulation of G0S2 (mitochondrial protein which promotes apoptosis via BCL2) and ID4 (related to decreased cell proliferation).In a different study, two of the transcripts that showed a decline in representation in GV oocytes with advancing age were GPX1 and PRDX1, which play a vital role in safeguarding cells against oxidative damage [23].

Fertilisation
For the female and male gametes to interact, the sperm needs to overcome the different barriers that the oocyte presents, namely the cumulus cells and the zona pellucida (ZP) [32].The zona pellucida is a glycoprotein matrix synthesised by the oocyte and surrounds it.ZP3 glycoprotein interacts with receptors in the sperm membrane which will lead to the fusion of its membrane to the oolema.Fusion of membranes will trigger molecular changes using calcium as a second messenger, resulting in meiosis II resumption and fusion of pronuclei.mRNA expression of ZP genes (ZP1-4) in 98 oocytes at different maturation stages, showed a significant decrease in ZP 1, 2 and 4 together with a non-significant decrease in ZP3 expression from GV to MII-stages [14].
Female age has shown a differential transcriptomes in human oocytes [13].Increased in expression for the younger groups, ANXA5 codes for a protein which interacts with protein kinase C, a key regulator of fertilisation events.Increased expression of PRRG1, a calcium ion binding protein gene, was found in older women which could Fig. 2 Cellular metabolism interactions.Many cellular processes need energy for their correct functioning, including spindle assembly and stability.Some genes have been shown to orchestrate mitochondria copy number replication, indispensable for homeostasis maintenance; whereas others play a role in β-oxidation and TCA cycle which could have a direct effect in DNA acetylation/ demethylation.Original diagram, Created with BioRender.comimpair fertilisation events.Similarly, gene expression alterations induced after cytoplasmic transfer from a mature to an immature oocyte could lead to calcium impairment, which could lead to fertilisation failures [10].Because of its involvement in the subcortical maternal complex, ECAT1 expression levels could ascertain the fertilisation potential in oocytes, as correct pronuclear formation has been seen to decrease from 84 to 54% when ECAT1 gene was silenced [12].

Embryo development
Oocyte-to-embryo transition is nature's masterpiece involving syngamy of the gametes, genetic combination, orchestrated synchrony of divisions, cell fusion, cellular differentiation, expansion and hatching which culminates in embryonic genome activation (EGA).The key regulators coordinating this transition and EGA in human continue to be weakly understood [33].Upon fertilisation, the zygote will divide to form an embryo and by day 3 of embryo development, human embryos ought to have six to eight cells.Because of its role in maintaining the accuracy of spindle assembly, impairment of genes such ECAT1 result in reduced cleavage rates (abnormal divisions) [11].Hence ECAT1 disruption was not only associated with compromised maturation but also with embryos which fail to develop.Interestingly, analysis of 39 oocytes from 24 women showed that body composition may influence mRNA stability and that obesity leads to an upregulation of proinflammatory-related transcripts in oocytes, which in turn result in altered gamete and embryo development [15].
A study analysing oocytes, cleavage embryos and blastocysts revealed that for some proteins which are initially maternally derived, mRNA expression could sustain their concentration past EGA [12].Immunofluorescence for PLAC8 protein showed its presence at beyond the morula stage, although PLAC8 mRNA expression was not detected in MII oocytes or cleavage stage embryos (PLAX8 protein was detected in MII).This protein has been appointed as a potential biomarker of implantation potential as negative outcomes are associated with no protein detection [12].PLAC8 protein could be related to expansion process once embryos implant.

Discussion
The present review highpoints the degree of orchestration of different processes, such as cell cycle progression, cellular metabolism and activation for zygotic/embryonic transcription, in order to establish human oocyte quality.
Looking at oocyte transcriptome, it has been established that its maturation stage was the main factor defining internal composition with almost 6,000 genes differentially expressed between GV and MII stages [21].The same group identified around 450 genes uniquely expressed in single stages.Although the presence of some transcripts may naturally happen due to progression and arrest of the cell cycle, others have been shown to be susceptible to external factors such as female age, obesity and or medical conditions (i.e.endometriosis).This draws scientists to question how much of oocyte quality is established from start ("nature") and how much relates to cell plasticity changes in response to external factors during development ("nurture") as it has been shown that mature oocytes have been found to be surrounded by cumulus cells with distinct gene expression profiles [14].
As female age increases, the percentage of poor-quality oocytes also increases, starting at 50% at 20 years of age and reaching 95% at 35 years of age [34].Literature reviewed in this article has illustrates the relationship between patient demographics and chromosome missegregation, perturbations of nuclear envelope and premature maturation.Furthermore, alterations in metabolic pathways have been described to affect maturation and genetic makeup of oocytes [35,36].The present work has reviewed literature showing how some genes related to mitochondrial activity show upregulation in mature stages, compared to immature oocytes.Nevertheless, in vitro maturation of non-competent oocytes may not be a viable option at present as such matured eggs showed some degree of mitochondrial function impairment.Recent mouse model research suggests that supplementing growth hormone during in vitro maturation (IVM) of oocytes could be a potential strategy to improve the success rate of ART by reducing cAMP levels, promoting mitochondrial function, reducing DNA damage and apoptosis [37].Recent literature has provided improved IVM protocols such as two phase IVM with pre-maturation steps, e.g.initial GV arrest followed by in vitro maturation using EGF-like growth factors or CNP peptide [38][39][40].Such systems, have reported a significantly improved maturation and clinical pregnancy rates versus standard IVM in certain patient cohorts.
Cytoplasmic transfer (CT), from a mature oocyte to an oocyte with cytoplasmic alterations, has been proposed as a technique to restore normal growth and function.Although further evidence is still required, this may only be relevant when performed between two mature oocytes.Hoseini et al., 2016 suggested that such technique was not effective to restore cytoplasmic maturity of recipient GV oocytes [10].
Interestingly, some genes (i.e.ECAT1) found in oocytes were identified to be relevant not only during maturation but also during embryo development.Moreover, literature has illustrated how some maternally inherited proteins (i.e.PLAC8) are dynamic and expression may be found across oocyte and embryo development.Such studies have described how protein expression may not be necessarily related to mRNA expression.Although, measure of RNA levels up to day 3 of embryo development is not direct proof of function as this RNA is silent.Recently, new methodologies have combined transcriptome and translatome sequencing to study gene expression in oocytes.Research has found that translatome could be more accurate measure of gene expression than transcriptome, especially in cells that undergo translational regulation like oocytes [41].

Table 1
Summary of the selected studies.Purpose, methodology, content, and findings are described for each of the studies, together with their corresponding KMET score